First Patient-to-Patient Intrahospital Transmission of Clade I Candida auris in France Revealed after a Two-Month Incubation Period

ABSTRACT Candida auris is a recently described emerging pathogen in hospital settings. Five genetic clades have been delineated, with each clade being isolated from specific geographic regions. We here describe the first transmission between 2 patients (P0 and P1) of a clade I C. auris strain imported into our burn intensive care unit from the Middle East. The strains have been investigated with whole-genome sequencing, which validated the high similarity of the genomes between isolates from P0 and P1. We repeatedly screened the two patients and contact patients (i.e., other patients present in the same hospital ward at the time of the first positive sample from P0 or P1; n = 49; 268 tests) with fungal culture and a C. auris-specific quantitative PCR assay to assess transmission patterns. We observed that P1 developed C. auris colonization between 41 and 61 days after potential exposure to P0 contamination, despite three negative screening tests as recommended by our national authorities. This study illustrates that transmission of C. auris between patients can lead to long-term incubation times before the detection of colonization. The recommended screening strategy may not be optimal and should be improved in the light of our findings. IMPORTANCE While large outbreaks of C. auris in hospital settings have been described, few clear cases of direct transmission have been documented. We here investigated the transmission of C. auris clade I between two patients with a 41- to 61-day delay between exposure and the development of colonization. This may lead to changes in the recommendations concerning treatment of C. auris cases, as an incubation period of this length is one of the first to be reported.

Re: Spectrum01833-22R1-A (First patient-to-patient intra-hospital transmission of a Clade I C. auris in France revealed after a two-months incubation period) Dear Prof. Alexandre Alanio: As you will read from the reviewers comments, there was some disagreement on the need for additional revisions. Reviewer 1 raises some important points regarding the strength of the conclusion that person-to-person transmission is the most likely mechanism. I think it would be best to soften this conclusion and provide a balanced commentary on alternate mechanisms in the revision. You may also want to soften a call for additional testing by suggesting that these approaches might provide reasonable approaches that could be studied in the future. The latter was also raised by reviewer 2. Careful attention to these comments as well as the other more minor issues is in order.
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The manuscript "First patient-to-patient intra-hospital transmission of a Clade I C. auris in France revealed after a two-months incubation period" by Alanio, et al., describes the first two patients with C.auris in a burn ICU. One of these patients had a positive blood culture and the other was colonized. The manuscript focuses on the kinetics of colonization of the second patient and argues that "person to person transmission" occurred but that the second patient had a prolonged incubation period prior to detection of colonization. The authors present data that the second patient (P1) had a series of negative qPCR screening tests prior to becoming colonized. They report "It took more than 41 days for C. auris to significantly colonize the body of P1 and be finally detectable on all sites despite three negative weekly screening tests." The limited number of SNPs between the two strains strongly supports the conclusion that the patients both had highly related strains that almost certainly had a common source. The first patient (P0) was mostly likely colonized on admission; this is the most likely source of the isolate. The fact that the patients' isolates are related does not mean that there was "patient-to-patient" transmission of the organism. The authors cite many references and present their own data that C.auris persists on environmental surfaces for weeks to months. It can also be found on the hands of healthcare workers. The authors do not describe any direct contact between P0 and P1. It is far more likely that P1 acquired C.auris via nosocomial horizontal transmission related to environmental contamination with C.auris. This is by far the most frequently described mechanism of hospital-acquired C.auris and the simplest explanation for this transmission event. This mechanism of transmission is central to the manuscript because the authors conclude that P1 was colonized/infected with C.auris 41-61 days prior to P1's positive tests because that is the window of time when both P0 and P1 were hospitalized. There is no data to support a prolonged "incubation period" in P1. More likely, the environment was contaminated with C.auris from P0 and this contamination persisted long after P0 was discharged. P1 could have acquired colonization with C.auris from the environment at any time prior to P1's positive tests.
Other concerns include: 1. The manuscript still contains many phrases that are difficult to follow. 2. The authors refer to their institutional policies on C.auris surveillance in the text. These policies should be provided as supplemental material. 3. References 13-16 are various agency guidelines about C.auris infection prevention. Links to these guidelines or more specific information about where the reader can access the guidelines should be included. Reference 15 doesn't provide any source for the guideline. 4. The authors recommend that patients be screened at more sites than in their institutional guidelines and with culture techniques in addition to qPCR techniques without providing evidence to support this conclusion.
Reviewer #2 (Comments for the Author): The authors have addressed the comments of prior review. The manuscript is easy to follow and interesting. I have the few suggestions for clarifications that would be helpful for the reader.
Were patients P0 and P1 negative for C. auris prior to the study, or untested?
Were other patients routinely screened on the floor/unit/building?
The authors suggest guideline changes may be needed. What guideline changes would they suggest and what type of cost may be associated?
Staff Comments:

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Spectrum01833-22R2
Editor As you will read from the reviewers comments, there was some disagreement on the need for additional revisions. Reviewer 1 raises some important points regarding the strength of the conclusion that person-to-person transmission is the most likely mechanism. I think it would be best to soften this conclusion and provide a balanced commentary on alternate mechanisms in the revision. You may also want to soften a call for additional testing by suggesting that these approaches might provide reasonable approaches that could be studied in the future. The latter was also raised by reviewer 2. Careful attention to these comments as well as the other more minor issues is in order.
Reply: Thank you for time and your comments. We responded to all reviewer's comments and modified the manuscript accordingly. This improved clearly the discussion. We hope that our manuscript will be accepted based on our revised version. Sincerely,

Pr Alexandre Alanio
Reviewer #1 (Comments for the Author): The manuscript "First patient-to-patient intra-hospital transmission of a Clade I C. auris in France revealed after a two-months incubation period" by Alanio, et al., describes the first two patients with C.auris in a burn ICU. One of these patients had a positive blood culture and the other was colonized. The manuscript focuses on the kinetics of colonization of the second patient and argues that "person to person transmission" occurred but that the second patient had a prolonged incubation period prior to detection of colonization. The authors present data that the second patient (P1) had a series of negative qPCR screening tests prior to becoming colonized. They report "It took more than 41 days for C. auris to significantly colonize the body of P1 and be finally detectable on all sites despite three negative weekly screening tests." The limited number of SNPs between the two strains strongly supports the conclusion that the patients both had highly related strains that almost certainly had a common source. The first patient (P0) was mostly likely colonized on admission; this is the most likely source of the isolate. The fact that the patients' isolates are related does not mean that there was "patient-to-patient" transmission of the organism. The authors cite many references and present their own data that C.auris persists on environmental surfaces for weeks to months. It can also be found on the hands of healthcare workers. The authors do not describe any direct contact between P0 and P1.
It is far more likely that P1 acquired C.auris via nosocomial horizontal transmission related to environmental contamination with C.auris. This is by far the most frequently described mechanism of hospital-acquired C.auris and the simplest explanation for this transmission event.
This mechanism of transmission is central to the manuscript because the authors conclude that P1 was colonized/infected with C.auris 41-61 days prior to P1's positive tests because that is the window of time when both P0 and P1 were hospitalized. There is no data to support a prolonged "incubation period" in P1. More likely, the environment was contaminated with C.auris from P0 and this contamination persisted long after P0 was discharged. P1 could have acquired colonization with C.auris from the environment at any time prior to P1's positive tests.
Reply: We agree with reviewer that contamination from the environment is a very likely hypothesis. We were not clear enough in our manuscript. Action: We modified the first chapter of the discussion to make Reviewer's hypothesis clearly stated and discussed line 149-171: " We describe here the kinetics of colonization to C. auris of one patient in a burn ICU who acquired Clade I strain from another patient who was admitted most probably with C. auris colonization. It took more than 41 days for C. auris to detect colonization of P1 and to be finally detectable on all sites despite three negative weekly screening tests. It is clear from the genetic analysis revealing a low number of SNPs between P0 and P1 strains (n<12), as already described in outbreak investigations (17), that the P0 strain have been transmitted to P1. Beyond this analysis, two likely scenarios coexist: (i) the contamination of P1 could have occur at very early steps after admission, at the time where P0 was not known to be C. auris-positive (Figure 1) either by a contaminated shared material or by healthcare worker hands, since no contact between patients was possible in ICU ; (ii) Some C. auris persisted in the environment allowing P1 contamination either early or later on, leading to C. auris detection after a period of 41 days. The latter seems less probable, as hygiene measures using C. auris efficient cleaning solution have been extensively used in P0's room, including cleaning of shared material and considering that all environmental samples came back negative in culture. In addition, no other contact patient was detected positive, suggesting that no environmental source was significantly persisting. We identified potential environmental sources of C. auris such as the bed and its mattresses but were never able to get a culture-positive environmental samples, suggesting that other routes of transmission were still plausible. These includes transmission through the hands of the healthcare workers, as previously shown (9, 12), through the sharing of material (echography machine) or very early before the first alert preventing finding the route of transmission. Indeed, it is possible that transmission could have occurred during the 7 days were both patients were hospitalized in parallel before the first recovery of C. auris in Patient 0 ( Figure 1) and before an extensive and adapter cleaning procedure could be done".
Other concerns include: 1. The manuscript still contains many phrases that are difficult to follow.